Strange crease being formed from filling face?
It looks like it's a harsh transition between normals.  You can get this even on the flattest of planes if the normals point in different directions:



it can happen easily when you're joining two separate areas like that, because it's not always immediately obvious which way Blender thinks the geometry faces. 

Fortunately it's super easy to fix, if that's your issue...just select all faces, then go to Mesh->Normals->Recalculate Outside, and Blender should make all the normals face properly:



If Blender makes it inside out, you can just use Flip Normals (or Recalculate Inside) to flip it.

EDIT: To explain normals -

Normals are a vector that is always* perpendicular to a face. In computer graphics, they're used to decide how to shade the face, based on the angle of the light vs. the angle of the normal. If the normal is directly pointed at a light, the face will be completely bright, and obviously if it's facing away from a light it'll be dark.

If you think of an object, like a vase for example, the outside of the vase is mostly bright because it's exposed to light. However, if you look inside the vase, it's mostly dark because no light gets in there:



If you model a vase, and part of the outside is marked as inside, or vice versa, it'll look really weird. This is what you're seeing, because Blender tries to figure out which way the normal should face based on how you model it. If you model two pieces separately and then join together, Blender might've thought one of the pieces faced inward and the other outward.

If you use Flat shading, it doesn't matter (as much) which direction a face points because each polygon has its own color/value, and its own normal:



In Smooth shading, Blender tries to average the normals so you get nice shading across the model. This is why I put a * next to "always" above, because the normals at the vertices of the face can point in other directions besides perpendicular so that the color blends smoothly from one face to another. You can imagine then that trying to average opposite values won't work well, and that causes artifacts like what you experienced:



Recalculate Normals then tells Blender to try to figure out which direction the normals SHOULD face:



Much better.  Those few faces on the edges that have sharp edges are just because it can't do miracles if there aren't enough faces.  An Subdivision modifier would smooth those out, but it WON'T smooth out the flipped normals.

I also put the * next to "always" because you can purposely mess with the normals to get lighting effects. For example, that's how normal mapping works (hence the name). It moves the normals around to give the illusion of bumps or patterns on the surface that aren't really there.

Hope this helps!